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conda_execution.md

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Conda based execution

You can run the MAGMA pipeline using the Conda based package manager to install all the prerequisite softwares.

The conda environments are expected by the conda_local profile of the pipeline, to be created within MAGMA/conda_envs directory

NOTE If you do have access to Singularity or Podman, then owing to their compatibility with Docker, you can still use the MAGMA Docker containers mentioned docker.config.

You can use the conda based setup for the pipeline for running MAGMA

  • On a local linux machine (e.g. your laptop or university server)
  • On an HPC cluster in case you don't have access to container systems like Singularity, Podman or Docker

Steps to setup the pipeline locally

NOTE These steps are only necessary if you don't have access to any container system, then therefore you'd need to install all softwares using the conda package manager.

  1. Copy the environment files from conda_envs folder locally
$ git clone https://github.com/TORCH-Consortium/MAGMA

$ cd MAGMA
  1. After cd in the conda_envs folder and execute the following commands to create the env

TIP

  1. For faster installation process, please download mamba tool and replace conda with mamba in the above commands.
  2. The path -p should be customized as per you setup
$ conda env create -p magma-env-1 --file magma-env-1.yml

$ conda env create -p magma-env-2 --file magma-env-2.yml

Run the pipeline

  1. Customize the pipeline and process level settings in the default_params file

  2. From inside the MAGMA folder, invoke the pipeline

$ nextflow run main.nf -profile conda_local
  1. Use the -resume flag to continue from previously generated output files, rather than restarting the entire analysis.
$ nextflow run main.nf -profile conda_local -resume